You really can't talk about these civilizations as a group. The Maya and Aztecs had some contact and continuity, but they were as different as Chinese and Arabs in many ways.
The Incas were so isolated they weren't even aware of the civilizations of Mesoamerica to their north. They were also generally not as bloodthirsty, although they also practiced human sacrifice, if on a much smaller scale.
Historians today are generally agreed that the collapse of these civilizations was caused by the merging of the Old and New World disease ecosystems. The Spanish had the luck of walking into societies that were disintegrating anyway.
It is estimated that 90 to 95% of the population of the Americas died by 1600 as a result of Eurasian and African diseases.
But you make a good point. Overt violence and suppression of the natives by European explorers wasn't really the major cause of death among those peoples. They were exposed to diseases for which they had acquired no natural immunities, and they were decimated by the resultant plagues.
In the case of the Aztecs, their culture had stagnated anyway to a large extent. They re-energized their warrior culture by arranging mock raids on nearby tribes to "capture" their young men and sacrifice them.
And people thought Roman decadence was bloody ...